COPS3 Gene (Protein Coding)

COP9 Signalosome Subunit 3

GC17M017246
GIFtS:
40
The protein encoded by this gene possesses kinase activity that phosphorylates regulators involved in signal transduction. It phosphorylates I kappa-Balpha, p105, and c-Jun. It acts as a docking site for complex-mediated phosphorylation. The gene is located within the Smith-Magenis syndrome region on chromosome 17. Several transcript variants encoding different isoforms have be... See more...

Aliases for COPS3 Gene

Aliases for COPS3 Gene

  • COP9 Signalosome Subunit 3 2 3 5
  • CSN3 2 3 4
  • SGN3 2 3 4
  • JAB1-Containing Signalosome Subunit 3 3 4
  • COP9 Signalosome Complex Subunit 3 3 4
  • Signalosome Subunit 3 3 4
  • COP9 (Constitutive Photomorphogenic, Arabidopsis, Homolog) Subunit 3 2
  • COP9 Constitutive Photomorphogenic Homolog Subunit 3 (Arabidopsis) 2
  • COP9 Constitutive Photomorphogenic Homolog Subunit 3 3
  • COP9 Complex Subunit 3 3
  • COPS3 5

External Ids for COPS3 Gene

Previous GeneCards Identifiers for COPS3 Gene

  • GC17M017465
  • GC17M018509
  • GC17M017093
  • GC17M017350
  • GC17M017090
  • GC17M016903
  • GC17M017151

Summaries for COPS3 Gene

Entrez Gene Summary for COPS3 Gene

  • The protein encoded by this gene possesses kinase activity that phosphorylates regulators involved in signal transduction. It phosphorylates I kappa-Balpha, p105, and c-Jun. It acts as a docking site for complex-mediated phosphorylation. The gene is located within the Smith-Magenis syndrome region on chromosome 17. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

GeneCards Summary for COPS3 Gene

COPS3 (COP9 Signalosome Subunit 3) is a Protein Coding gene. Diseases associated with COPS3 include Smith-Magenis Syndrome and Episodic Pain Syndrome, Familial, 3. Among its related pathways are Vesicle-mediated transport and Transcription-Coupled Nucleotide Excision Repair (TC-NER). An important paralog of this gene is PSMD3.

UniProtKB/Swiss-Prot Summary for COPS3 Gene

  • Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Gene Wiki entry for COPS3 Gene

Additional gene information for COPS3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COPS3 Gene

Genomics for COPS3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for COPS3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COPS3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COPS3

Top Transcription factor binding sites by QIAGEN in the COPS3 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • CREB
  • NRF-2
  • p300
  • p53

Genomic Locations for COPS3 Gene

Latest Assembly
chr17:17,246,616-17,281,303
(GRCh38/hg38)
Size:
34,688 bases
Orientation:
Minus strand

Previous Assembly
chr17:17,149,930-17,184,560
(GRCh37/hg19 by Entrez Gene)
Size:
34,631 bases
Orientation:
Minus strand

chr17:17,150,141-17,184,607
(GRCh37/hg19 by Ensembl)
Size:
34,467 bases
Orientation:
Minus strand

Genomic View for COPS3 Gene

Genes around COPS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COPS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COPS3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for COPS3 Gene

Proteins for COPS3 Gene

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  • Protein details for COPS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UNS2-CSN3_HUMAN
    Recommended name:
    COP9 signalosome complex subunit 3
    Protein Accession:
    Q9UNS2
    Secondary Accessions:
    • B2R683
    • B4DY81
    • O43191
    • Q7LDR6

    Protein attributes for COPS3 Gene

    Size:
    423 amino acids
    Molecular mass:
    47873 Da
    Quaternary structure:
    • Component of the CSN complex, composed of COPS1/GPS1, COPS2, COPS3, COPS4, COPS5, COPS6, COPS7 (COPS7A or COPS7B), COPS8 and COPS9 isoform 1 (PubMed:18850735, PubMed:26456823). In the complex, it probably interacts directly with COPS1, COPS4, COPS8 and COPS9 isoform 1 (PubMed:18850735, PubMed:26456823). Interacts with CK2 and PKD (PubMed:12628923). Interacts with the translation initiation factor EIF3S6 and IKBKG (PubMed:11418127, PubMed:12220626). Interacts with ERCC6 (PubMed:26030138).
    SequenceCaution:
    • Sequence=AAC14197.1; Type=Frameshift; Evidence={ECO:0000305};
    Miscellaneous:
    • Amplified and overexpressed in some osteosarcomas (OS), suggesting that it may participate in TP53 degradation in OS.

    Three dimensional structures from OCA and Proteopedia for COPS3 Gene

    Alternative splice isoforms for COPS3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COPS3 Gene

Protein Expression for COPS3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for COPS3 Gene

  • Ubiquitination at Lys30, Lys125, Lys243, Lys254, Lys281, Lys296, Lys312, Lys366, Lys382, Lys391, and Lys406
  • Modification sites at PhosphoSitePlus

Other Protein References for COPS3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COPS3 Gene

Domains & Families for COPS3 Gene

Gene Families for COPS3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for COPS3 Gene

InterPro:
Blocks:
  • Domain in components of the proteasome, COP9-complex and eIF3 (PCI)
ProtoNet:

Suggested Antigen Peptide Sequences for COPS3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ79299, highly similar to COP9 signalosome complex subunit 3 (B4DY81_HUMAN)
  • JAB1-containing signalosome subunit 3 (CSN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UNS2

UniProtKB/Swiss-Prot:

CSN3_HUMAN :
  • Belongs to the CSN3 family.
Family:
  • Belongs to the CSN3 family.
genes like me logo Genes that share domains with COPS3: view

Function for COPS3 Gene

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  6. Cell Lines for research

Molecular function for COPS3 Gene

UniProtKB/Swiss-Prot Function:
Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.
GENATLAS Biochemistry:
COP9 (constitutive photomorphogenic,Arabidopsis) homolog subunit 3,ubiquitously expressed,predominantly in cardiac and skeletal muscle,involved in signal transduction,within the Smith-Magenis critical region

Phenotypes From GWAS Catalog for COPS3 Gene

Gene Ontology (GO) - Molecular Function for COPS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11418127
genes like me logo Genes that share ontologies with COPS3: view
genes like me logo Genes that share phenotypes with COPS3: view

Animal Models for COPS3 Gene

MGI Knock Outs for COPS3:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COPS3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for COPS3 Gene

Localization for COPS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COPS3 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COPS3 gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 2
plasma membrane 1
extracellular 1
cytoskeleton 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COPS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IEA,TAS 9535219
GO:0005829 cytosol IDA,TAS --
GO:0008180 COP9 signalosome IEA,IDA 18850735
genes like me logo Genes that share ontologies with COPS3: view

Pathways & Interactions for COPS3 Gene

genes like me logo Genes that share pathways with COPS3: view

SIGNOR curated interactions for COPS3 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for COPS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000338 protein deneddylation IDA 19141280
GO:0000715 nucleotide-excision repair, DNA damage recognition TAS --
GO:0001701 in utero embryonic development IEA --
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0006511 ubiquitin-dependent protein catabolic process IBA 21873635
genes like me logo Genes that share ontologies with COPS3: view

Drugs & Compounds for COPS3 Gene

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No Compound Related Data Available

Transcripts for COPS3 Gene

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mRNA/cDNA for COPS3 Gene

7 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
18 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COPS3

Alternative Splicing Database (ASD) splice patterns (SP) for COPS3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a ·
SP1: - - - - -
SP2: - - - - -
SP3: - - - - - -
SP4: - -
SP5: -
SP6: - -
SP7: - - - - - -
SP8:
SP9: - - -
SP10: -
SP11: - -
SP12:

ExUns: 14b · 14c · 14d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for COPS3 Gene

GeneLoc Exon Structure for
COPS3

Expression for COPS3 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COPS3 Gene

mRNA expression in normal human tissues for COPS3 Gene
mRNA expression by GTEx for COPS3 GenemRNA expression by BioGPS for COPS3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COPS3 Gene

This gene is overexpressed in Muscle - Skeletal (x4.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COPS3 Gene



Protein tissue co-expression partners for COPS3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COPS3

SOURCE GeneReport for Unigene cluster for COPS3 Gene:

Hs.6076

mRNA Expression by UniProt/SwissProt for COPS3 Gene:

Q9UNS2-CSN3_HUMAN
Tissue specificity: Widely expressed. Expressed at high level in heart and skeletal muscle.

Evidence on tissue expression from TISSUES for COPS3 Gene

  • Nervous system(4.8)
  • Blood(4.4)
  • Lung(4.3)
  • Liver(4.3)
  • Skin(2.2)
  • Bone marrow(2.2)
genes like me logo Genes that share expression patterns with COPS3: view

No data available for Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for COPS3 Gene

Orthologs for COPS3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for COPS3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia COPS3 30 31
  • 99.76 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia COPS3 31
  • 99 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia COPS3 31
  • 99 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia COPS3 30 31
  • 93.7 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Cops3 30 17 31
  • 91.88 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Cops3 30
  • 91.25 (n)
Cow
(Bos Taurus)
 Mammalia COPS3 30 31
  • 86.6 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves COPS3 30 31
  • 87.63 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia COPS3 31
  • 89 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia cops3 30
  • 82.27 (n)
Str.11176 30
African clawed frog
(Xenopus laevis)
 Amphibia cops3-prov 30
Zebrafish
(Danio rerio)
 Actinopterygii cops3 30 31
  • 78.41 (n)
 OneToOne
wufk59f01 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.684 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006445 30
  • 57.29 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CSN3 30 31 32
  • 56.24 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea csn-3 31
  • 19 (a)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons COP13 30
  • 48.92 (n)
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.7012 30
Rice
(Oryza sativa)
 Liliopsida Os08g0119000 30
  • 52.45 (n)
Wheat
(Triticum aestivum)
 Liliopsida Ta.2898 30
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.1915 30
Species where no ortholog for COPS3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for COPS3 Gene

ENSEMBL:
Gene Tree for COPS3 (if available)
TreeFam:
Gene Tree for COPS3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COPS3: view image

Paralogs for COPS3 Gene

Paralogs for COPS3 Gene

Pseudogenes.org Pseudogenes for COPS3 Gene

genes like me logo Genes that share paralogs with COPS3: view

Variants for COPS3 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COPS3 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs11549132 Benign: not provided 17,281,181(-) C/T
NM_003653.4(COPS3):c.6G>A (p.Ala2=) 		SYNONYMOUS_VARIANT,FIVE_PRIME_UTR
rs553573176 Likely Benign: not provided 17,249,049(-) G/A
NM_003653.4(COPS3):c.1024-10C>T 		INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for COPS3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for COPS3 Gene

Variant ID Type Subtype PubMed ID
esv3640124 CNV gain 21293372
nsv155 OTHER inversion 15895083
nsv469777 CNV gain 16826518
nsv499114 OTHER inversion 21111241
nsv833380 CNV loss 17160897
nsv833382 CNV loss 17160897
nsv9499 CNV gain 18304495

Variation tolerance for COPS3 Gene

Residual Variation Intolerance Score: 21.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.53; 11.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COPS3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COPS3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COPS3 Gene

Disorders for COPS3 Gene

MalaCards: The human disease database

(14) MalaCards diseases for COPS3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
smith-magenis syndrome
  • sms
episodic pain syndrome, familial, 3
  • feps3
bone angioendothelial sarcoma
  • osseous hemangiosarcoma
juxtacortical osteosarcoma
  • parosteal osteogenic sarcoma
peripheral osteosarcoma
  • surface osteosarcoma
- elite association - COSMIC cancer census association via MalaCards
Search COPS3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for COPS3

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with COPS3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for COPS3 Gene

Publications for COPS3 Gene

  1. Association of the mammalian proto-oncoprotein Int-6 with the three protein complexes eIF3, COP9 signalosome and 26S proteasome. (PMID: 12220626) Hoareau Alves K … Jalinot P (FEBS letters 2002) 3 4 23
  2. Subunit 3 of the COP9 signal transduction complex is conserved from plants to humans and maps within the smith-magenis syndrome critical region in 17p11.2. (PMID: 10191102) Potocki L … Lupski JR (Genomics 1999) 2 3 4
  3. A novel protein complex involved in signal transduction possessing similarities to 26S proteasome subunits. (PMID: 9535219) Seeger M … Dubiel W (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1998) 2 3 4
  4. Identification of Novel Proteins Co-Purifying with Cockayne Syndrome Group B (CSB) Reveals Potential Roles for CSB in RNA Metabolism and Chromatin Dynamics. (PMID: 26030138) Nicolai S … Proietti-De-Santis L (PloS one 2015) 3 4
  5. CSNAP Is a Stoichiometric Subunit of the COP9 Signalosome. (PMID: 26456823) Rozen S … Sharon M (Cell reports 2015) 3 4

ExternalLinks

View latest publications for COPS3 gene in Mastermind

Products for COPS3 Gene

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Sources for COPS3 Gene